Molecular
preferences
One thing modeling may illuminate is the role of DNA structure in amiloride's binding preference. DNA, Venanzi explains, is a far cry from the textbook depictions of a symmetrical double helix with perfectly parallel base pairs. In real life the molecule is more floppy and irregular. "The alignment can change based on the flanking sequences--the base pairs on either side of the binding site," Venanzi says. This introduces slight kinks and twists in the structure of the DNA molecule. Perhaps, Venanzi suggests, amiloride finds it easier to bind to the particular twists and turns in AT-rich sequences.
| Check out the AMBER website. Venanzi says: "This site is of interest to those running AMBER (like us). It is professionally maintained by many people and has a mailing list. For anyone who wants to do calculations on DNA or proteins, this site is invaluable." |
Venanzi also plans to explore the quantum mechanical realm of amiloride binding in collaboration with William Skawinski, a senior research associate in her laboratory and a lecturer in chemistry at New Jersey Tech. So-called stacking interactions occur between electrons in the amiloride molecule and those in the base pairs that amiloride slices between when it binds. These interactions may affect the relative alignment of amiloride and DNA and how well they bind to each other. Computer simulations of amiloride binding to pairs of DNA bases should reveal if the stacking interactions play an important role, Venanzi says.
Once Venanzi gets some insights into how these structural and electrostatic forces come into play, she can test them experimentally. Given a range of hexamers of different compositions, she says, it should be possible to predict which ones amiloride will most prefer to bind to. Then she will team up with Neocles Leontis, a chemist at Bowling Green State University in Ohio, who will use nuclear magnetic resonance spectroscopy to study the binding of amiloride to real hexamers. "This way we should be able to see if our predictions are correct and learn more about the details of amiloride's binding preference at the molecular level."
This research is funded by the American Chemical Society.
